We would be able to say more if we knew exactly what your actual idea for your thesis is. But based on the information you've given us, we know that your essay will be comparing/contrasting literary elements, such as narrator, point of view, and theme, as well as some literary techniques with the ultimate purpose of drawing a larger conclusion about the two short stories. So long as your thesis uses the comparisons and contrasts to draw a larger conclusion about the works that goes above and beyond what you are comparing and contrasting, your essay should come out very interesting. Organization, meaning in what order you decide to talk about these devices of elements and techniques does not wholly matter. So long as the organization makes sense and is logical, you'll be fine. You can even decide to rearrange paragraphs once your first draft is finished. But what does matter is understanding that you always have two options for a comparison and contrast essay.
The first method of organization you can choose from is topic-by-topic. With this method, you will be using one paragraph to speak on one topic of comparison for one work, a second paragraph to speak on the same topic for the second work, followed by a third paragraph to actually do the comparison/contrasting, meaning point out exactly what the differences are and why they are significant, especially how they address your thesis. For example, if you were to write one paragraph describing the narration style in "The Yellow Wallpaper," your next paragraph would describe the similar narration style in "Two Kinds." Finally, you would use a third paragraph to actually talk about how the narration styles are different in both works and to further say exactly why those differences are important, especially how they address/prove your thesis. The advantage of topic-by-topic organization is that you will very quickly reach your word count goal without having to talk about too many topics. A word count of 2,000 is about 8 pages double spaced. You could use this method of organization and reach that goal through talking about four topics. However, a disadvantage is that this method won't work very well if you don't have enough to say about each topic.
The second organizational method is referred to as point-by-point. With this method, you would be comparing and contrasting your points or topics for both works in the same paragraph. For example, you would write one paragraph describing the narration techniques in both "The Yellow Wallpaper" and "Two of a Kind," plus in this same paragraph you would be explaining the similarities and differences and especially be stating exactly why these similarities and differences are important and how they prove your thesis. One advantage to using this organizational style is that you could talk about a lot of different points in one paragraph. Say, for example, you didn't have enough to say about individual literary elements, like diction and syntax, to be able to write a full paragraph. No problem. You could talk about several literary elements in the same paragraph by using literary elements as your topic sentence. The disadvantage of this organizational method is that you would need more points, about 12 to maybe 14 points, to talk about to reach your word goal.
So at this point, what you should do is make a list of all the points you want to talk about in order to prove your thesis. Then under each point on your list, write out the details you can talk about to help you prove that the element/technique exists and also how it proves your thesis. Once you have a broader idea of what can be said, you can then narrow things down further to what actually needs to be said, which will help you decide which of the two organizational methods will work best for you for this particular paper. Once you've picked out your method, without worrying too much at this point about what order to say things in, you can then make your outline.